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pb_force.f
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pb_force.f
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! <compile=optimized>
#include "copyright.h"
#define _REAL_ double precision
#define REQUIRE(e) if(.not.(e)) call croak(__FILE__,__LINE__)
#include "pb_def.h"
#include "timer.h"
module poisson_boltzmann
implicit none
# include "pb_constants.h"
! PBMD parameters
_REAL_, parameter :: pbkb = 1.3807D-23 / 1.6606D-27 / (1.00D+12)**2 * (1.00D+10)**2
_REAL_, parameter :: fioni = 6.0220D+23 / 1.00D+30
_REAL_, parameter :: fiono = ONE / fioni
_REAL_, parameter :: eps0 = 8.8542D-12 / (1.6022D-19)**2 / (1.00D+10)**3 * (1.00D+12)**2 * 1.6606D-27
_REAL_, parameter :: frcfac = 0.01D0 / 4.1840D0
! PBMD FD control variables
logical :: outphi
logical :: srsas
logical :: scalerf
integer :: phiform
integer :: saopt
integer :: sasopt
integer :: dbfopt
integer :: eneopt
integer :: npbopt
integer :: solvopt
integer :: frcopt
integer :: intopt
integer :: bcopt
integer :: smoothopt
integer :: xm
integer :: ym
integer :: zm
integer :: xmym
integer :: xmymzm
integer :: nbuffer
integer :: level
integer :: nfocus
integer :: fscale
integer :: maxitn
integer :: itn
integer :: m, n
integer :: savbcopt(MAXLEVEL)
integer :: levelblock(MAXLEVEL)
integer :: savxm(MAXLEVEL)
integer :: savym(MAXLEVEL)
integer :: savzm(MAXLEVEL)
integer :: savxo(MAXLEVEL) !Origin offset
integer :: savyo(MAXLEVEL) !
integer :: savzo(MAXLEVEL)
integer :: savxmym(MAXLEVEL)
integer :: savxmymzm(MAXLEVEL)
integer :: isurfchg ! print surface charges
_REAL_ :: h
_REAL_ :: gox
_REAL_ :: goy
_REAL_ :: goz
_REAL_ :: fmiccg
_REAL_ :: accept
_REAL_ :: laccept
_REAL_ :: wsor
_REAL_ :: lwsor
_REAL_ :: norm
_REAL_ :: inorm
_REAL_ :: xmax
_REAL_ :: xmin
_REAL_ :: ymax
_REAL_ :: ymin
_REAL_ :: zmax
_REAL_ :: zmin
_REAL_ :: gxmax
_REAL_ :: gxmin
_REAL_ :: gymax
_REAL_ :: gymin
_REAL_ :: gzmax
_REAL_ :: gzmin
_REAL_ :: savxbox(MAXLEVEL)
_REAL_ :: savybox(MAXLEVEL)
_REAL_ :: savzbox(MAXLEVEL)
_REAL_ :: cxbox(MAXLEVEL)
_REAL_ :: cybox(MAXLEVEL)
_REAL_ :: czbox(MAXLEVEL)
_REAL_ :: savh(MAXLEVEL)
_REAL_ :: savgox(MAXLEVEL)
_REAL_ :: savgoy(MAXLEVEL)
_REAL_ :: savgoz(MAXLEVEL)
_REAL_ :: offx
_REAL_ :: offy
_REAL_ :: offz
_REAL_ :: fillratio
_REAL_ :: epsin
_REAL_ :: epsout
_REAL_ :: pbkappa
_REAL_ :: istrng
_REAL_ :: ivalence
_REAL_ :: pbtemp
_REAL_ :: totcrg
_REAL_ :: totcrgp
_REAL_ :: totcrgn
_REAL_ :: pbgamma_int
_REAL_ :: pbgamma_ext
! PBMD topology information
integer :: lastp
integer :: ngrdcrg
integer, allocatable :: icrd(:,:)
integer, allocatable :: grdcrg(:,:)
_REAL_, allocatable :: qgrdcrg(:)
_REAL_, allocatable :: gcrd(:,:)
_REAL_, allocatable :: acrd(:,:)
_REAL_, allocatable :: acrg(:)
_REAL_, allocatable :: gcrg(:,:)
! PBMD nblist information
integer :: maxnbr
integer :: maxnba
_REAL_ :: cutres, cutnb, cutfd, cutsa
integer, allocatable :: nshrt(:)
integer, allocatable :: nex(:)
integer, allocatable :: iex(:,:)
integer, allocatable :: iprlong(:)
integer, allocatable :: iprshrt(:)
integer, allocatable :: iar1pb(:,:)
_REAL_, allocatable :: cn1pb(:)
_REAL_, allocatable :: cn2pb(:)
_REAL_, allocatable :: cn3pb(:)
! PBMD cap water simulation information
integer :: mpopt
integer :: lmax
integer :: inatm
integer :: outwat
integer :: oution
integer, allocatable :: outflag(:)
integer, allocatable :: outflagorig(:)
integer, allocatable :: mapout(:)
integer, allocatable :: ibelly(:)
_REAL_ :: sepbuf
! physical variables for energy and force calculations
integer:: nbnd
integer:: nbndx
integer:: nbndy
integer:: nbndz
! physical variable maps for numerical solutions
_REAL_, allocatable :: phi(:)
_REAL_, allocatable :: bv(:)
_REAL_, allocatable :: chgrd(:)
_REAL_, allocatable :: epsx(:)
_REAL_, allocatable :: epsy(:)
_REAL_, allocatable :: epsz(:)
_REAL_, allocatable :: saltgrd(:)
! geometry maps for dielectric interface
integer, allocatable :: insas(:)
integer, allocatable :: atmsas(:)
_REAL_, allocatable :: lvlset(:)
_REAL_, allocatable :: zv(:)
! physical variable maps for force calculations
_REAL_, allocatable :: cphi(:)
integer, allocatable :: iepsav(:,:)
integer, allocatable :: iepsavx(:,:)
integer, allocatable :: iepsavz(:,:)
integer, allocatable :: iepsavy(:,:)
_REAL_, allocatable :: fedgex(:)
_REAL_, allocatable :: fedgey(:)
_REAL_, allocatable :: fedgez(:)
! saved phi array for pbmd
_REAL_, allocatable :: xs(:)
integer :: xsoffset
! ligand focusing options
logical :: ligand
character(len=256) ligandmask
integer, allocatable :: liveflag(:)
integer, allocatable :: realflag(:)
integer :: ntrajmol
_REAL_ :: buffer
! Multiple distributive fine grid geometry / Multiblock focusing
logical :: multiblock !TRUE if specified multiblock
logical :: firstleveldone !TRUE if level 1 is done once
integer, allocatable :: blkxo(:) !block origin in x dir
integer, allocatable :: blkyo(:) !block origin in y dir
integer, allocatable :: blkzo(:) !block origin in z dir
integer, allocatable :: blkxlo(:) !block lower bound in x
integer, allocatable :: blkylo(:) !block lower bound in y
integer, allocatable :: blkzlo(:) !block lower bound in z
integer, allocatable :: blkxup(:) !block upper bound in x
integer, allocatable :: blkyup(:) !block upper bound in y
integer, allocatable :: blkzup(:) !block upper bound in z
integer, allocatable :: blknx(:) !block grid length in x
integer, allocatable :: blkny(:) !block grid length in y
integer, allocatable :: blknz(:) !block grid length in z
integer, allocatable :: blknxny(:) !blknx . blkny
integer, allocatable :: blknynz(:) !blkny . blknz
integer, allocatable :: blknxnz(:) !blknx . blknz
integer, allocatable :: blknxnynz(:) !blknx . blkny . blknz
integer :: ngrdblkx !# of grids per block in x
integer :: ngrdblky !# of grids per block in y
integer :: ngrdblkz !# of grids per block in z
integer :: xmblk !total blocks in x
integer :: ymblk !total blocks in y
integer :: zmblk !total blocks in z
integer :: ilower !
integer :: iupper !
integer :: jlower !
integer :: jupper !
integer :: klower !
integer :: kupper !
integer :: nfirstwpad(MAXBLOCK+1) !Described in the text
integer :: nfirst0pad(MAXBLOCK+1) !Described in the text
integer :: nfirst4s3f(MAXBLOCK+1) !Described in the text
integer, allocatable :: lfocuswpad(:) !Described in the text
integer, allocatable :: lfocus0pad(:) !Described in the text
integer, allocatable :: lfocus4s3f(:) !Described in the text
integer, allocatable :: fineblockindex(:) !for load balancing
integer :: iblkdebug !
_REAL_, allocatable :: blkgox(:) !block origin in x
_REAL_, allocatable :: blkgoy(:) !block origin in y
_REAL_, allocatable :: blkgoz(:) !block origin in z
_REAL_, allocatable :: coarsephi(:) !saved 1st level solution
! _REAL_, allocatable :: spv(:) !Ion placement
integer :: saltout !Ion placement
logical :: outsalt !Ion placement
_REAL_ :: stern !Ion Placement
contains
!+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
!+ Driver of PBMD energy and forces
! call pb_force( natom,nres,ntypes,npdec,ix(i02),ix(i04),ix(i06),&
! ix(i10),cn1,cn2,xx(l15),x,f,evdw,eelt,epol)
subroutine pb_force( natom,nres,ntypes,npdec,ipres,iac,ico,natex,cn1,cn2,cg,x,f,enb,eel,eelrf )
use solvent_accessibility, only : dprob, radi, radip, radip2, radip3, nzratm, &
#ifdef SANDER
sa_init, sa_driver, sa_free, sa_free_mb
#else
#ifdef MPI
sa_init, sa_driver, sa_free, sa_free_mb, &
saslave_init
#else
sa_init, sa_driver, sa_free, sa_free_mb
#endif /* MPI */
#endif /*SANDER*/
use decomp, only : irespw, jgroup
use pbtimer_module
! Common variables
# include "pb_md.h"
#ifdef SANDER
# undef _REAL_
# include "../../../src/sander/md.h"
# include "../../../src/sander/box.h"
integer, parameter :: mytaskid = 0
integer, parameter :: numtasks = 1
#else /* SANDER */
# include "md.h"
# include "box.h"
#ifdef MPI
include "mpif.h"
# include "parallel.h"
#else /*MPI*/
integer, parameter :: mytaskid = 0
integer, parameter :: numtasks = 1
#endif /*MPI*/
#endif /* SANDER */
# include "extra.h"
! Passed variables
integer natom, nres, ntypes, npdec, ipres(*), iac(*), ico(*), natex(*)
_REAL_ cn1(*), cn2(*), cg(natom), x(3,natom), f(3,natom)
_REAL_ enb, eel, eelrf
! Local variables
integer i, j, k
integer iatm, proatm, atmfirst, atmlast
integer atmind(natom)
_REAL_ acg(natom)
_REAL_ pbcutcap, pbxcap, pbycap, pbzcap
_REAL_ eelrffd, eelrfmp
_REAL_ pbfrc(3,natom)
_REAL_ ionene
! Local multiblock variables
integer ipermute !
integer iblock !
! integer boolsorted
integer mynblock !
integer lvl2begin !
integer orphanblkn !
integer guess_int !
!#endif
integer ierr !
integer taskpiece !
integer myblkstart !
integer myblkend !
integer tasknatom !
integer ihavedone !
! readin info verification
integer tmp_nsatm !
integer mingrdblk !
integer myldim !
logical indexmatched !
!This is not an efficient way to use the memory, need to estimate
!the size of the array.
integer, allocatable :: tmpindex(:) !
_REAL_ myh !
_REAL_ guess_float !
_REAL_ blk_eelrffd ! temporary storage for eelrffd
_REAL_ blk_eel ! temporary storage for eel
_REAL_ blk_enb ! temporary storage for enb
#ifdef MPI
#ifndef SANDER
_REAL_ , allocatable :: recvbuf1(:), recvbuf2(:), recvbuf3(:)
#endif
#endif /*MPI*/
! end of multi-block
logical localpbgrid
! Variables initialization
enb = ZERO; eel = ZERO; eelrf = ZERO
eelrffd = ZERO; eelrfmp = ZERO
pbfrc = ZERO; ionene = ZERO
atmind = 0
! Variables initialization, multi-block
myblkstart = 0
myblkend = 0
ierr = 0
acg = ZERO !making sure clien(s) have clean acg
firstleveldone = .false.
#ifdef MPI
#ifndef SANDER
call pbslave_init(natom)
call saslave_init(natom)
#endif
#endif /* MPI */
!End of multi-block initializatioin
if ( ifcap /= 0 .and. (ifcap < 3 .or. ifcap > 5) ) then
pbcutcap = cutcap+TWO; pbxcap = xcap; pbycap = ycap; pbzcap = zcap
radi(-1) = pbcutcap; acrd(1,-1) = pbxcap; acrd(2,-1) = pbycap; acrd(3,-1) = pbzcap
radip3(1) = radi(-1); nzratm(1) = -1
else
pbcutcap = ZERO; pbxcap = ZERO; pbycap = ZERO; pbzcap = ZERO
end if
! split atoms into internal/external and update nblist
call pbtimer_start(PBTIME_PBLIST)
if ( pbgrid ) then
if( mpopt == 1 ) then
!multipole expansion (commented by mj)
call pb_atmpart(pbverbose,pbprint,natom,ibgwat,ienwat,ibgion,ienion, &
inatm,outwat,oution,ipres,outflag, &
pbxcap,pbycap,pbzcap,pbcutcap,sepbuf,x,ifcap)
else if ( ifcap == 2 ) then
! Use cutcap here, not pbcutcap because the latter is augmented by TWO
call pb_atmpart(pbverbose,pbprint,natom,ibgwat,ienwat,ibgion,ienion, &
inatm,outwat,oution,ipres,outflag, &
pbxcap,pbycap,pbzcap,cutcap,0.0d0,x,ifcap)
else if ( ifcap == 5 ) then
! Use cutcap here, not pbcutcap because the latter is augmented by TWO
call pb_atmpart2(pbverbose,pbprint,natom,ibgwat,ienwat,ibgion,ienion, &
inatm,outwat,oution,ipres,outflag, &
cutcap,x)
else if ( ligand ) then
! This option will be visited if it is not the first time pb_force got
! called, however there would be something to do here once we've done
! MD.
continue
else
! Multiblock will go here as well as other conditions
outflag = 0
end if
end if
call pb_atmconv(mpopt,ifcap,natom,ibgwat,ienwat,ibgion,ienion,atmind,ipres,x,cg,acg)
! This is for the global run for the coarse grid
! If ligand/multiple block is used, these will be updated later in docklist
if ( ntnba == 1 .and. max(cutnb,cutsa,cutfd) > ZERO ) call pb_atmlist(pbverbose,pbprint,&
maxnba,natom,ntypes,iac,ico,natex,nshrt,nex,iex,iar1pb,iprshrt,&
cutnb,cutsa,cutfd,cn1,cn2,cn1pb,cn2pb,cn3pb,cg,acrd(1,1))
if ( ntnbr == 1 ) ntnbr = 0
if ( ntnba == 1 ) ntnba = 0
call pbtimer_stop(PBTIME_PBLIST)
call pbtimer_start(PBTIME_PBSETUP)
if ( mpopt /=2 .and. pbgrid ) then
if ( ligand ) &
call pb_atmpart3(pbverbose,pbprint,natom,buffer,xmin,xmax,ymin,ymax,&
zmin,zmax,liveflag,realflag,outflag,x)
if (ifcap == 2 .or. ifcap == 5) then
call pb_setgrd(pbverbose,pbprint,pbinit,pbgrid,ifcap,1,inatm,pbxcap,pbycap,pbzcap,pbcutcap)
else
call pb_setgrd(pbverbose,pbprint,pbinit,pbgrid,ifcap,1,natom,pbxcap,pbycap,pbzcap,pbcutcap)
end if
end if
call pbtimer_stop(PBTIME_PBSETUP)
! compute grid-independent sas calculations for dielectric assignment
! when ifcap /= 0, no need to comptue sas
call pbtimer_start(PBTIME_PBSAS)
!write(600+mytaskid,*)natom,natom,ifcap,dprob,radi,radip,radip2,outflag;call mexit(0,0)
if ( srsas .and. ( ifcap == 0 .or. ifcap == 5 ) ) then
if( ifcap == 5 ) then
call sa_init(pbverbose,pbprint,natom,inatm,ifcap,dprob,radi,radip,radip2,outflag)
! the call here requires verification if we need to take care of multiblock as well
call sa_driver(pbverbose,pbprint,ipb,inp,natom,inatm,dosas,ndosas,npbstep,nsaslag,&
ligand, outflag,&
acrd(1,1),iar1pb(1,0),iprshrt,nex,iex)
else
call sa_init(pbverbose,pbprint,natom,natom,ifcap,dprob,radi,radip,radip2,outflag)
!write(600+mytaskid,*)ipb,inp,natom,natom,dosas,ndosas,npbstep,nsaslag,ligand,multiblock,outflag;call mexit(0,0)
call sa_driver(pbverbose,pbprint,ipb,inp,natom,natom,dosas,ndosas,npbstep,nsaslag,&
(ligand .or. multiblock), outflag,&
acrd(1,1),iar1pb(1,0),iprshrt,nex,iex)
end if
end if
call pbtimer_stop(PBTIME_PBSAS)
call pbtimer_start(PBTIME_PBLIST)
! Multi-block:
! Following part is for level 2 focusing task partition
if ( multiblock ) then
! Current task partitioning: Predetermined distribution
! o o o o For 4 simultaneous tasks doing 13 blocks, mytaskid
! o o o o 0, 1, 2 all get 3 blocks respectively. Mytaskid 3
! o o o o gets 4 blocks. Note: Queuing the blocks inside MPI
! o is a pain in the neck, so it's not in our future
! plan.
mynblock = levelblock(2)
taskpiece = levelblock(2)/numtasks
orphanblkn = levelblock(2)-taskpiece*numtasks
! doing serial
if ( numtasks < 2 ) then
myblkstart = 1
myblkend = mynblock
! doing parallel
else if ( orphanblkn == 0 .or. mytaskid < numtasks-orphanblkn ) then
myblkstart = mytaskid*taskpiece + 1
myblkend = (mytaskid+1)*taskpiece
else if ( mytaskid == numtasks-orphanblkn ) then
! when orphanblkn == 1, it adds one block to the last task
myblkstart = mytaskid*taskpiece+1
myblkend = (mytaskid+1)*taskpiece+1
else if ( mytaskid > numtasks-orphanblkn ) then
myblkstart = mytaskid*taskpiece+1+mytaskid+orphanblkn-numtasks
myblkend = (mytaskid+1)*taskpiece+1+mytaskid+orphanblkn-numtasks
else
write(6,*) "exception caught, block division error for MPI"
call mexit(6,1)
end if
if ( master ) then
do i = 1, numtasks
if ( orphanblkn == 0 .or. i < numtasks-orphanblkn ) then
write(6,*) "thread:",i,"is for",taskpiece ,"fine blocks."
else if ( i == numtasks-orphanblkn ) then
write(6,*) "thread:",i,"is for",taskpiece+1,"fine blocks."
else if ( i > numtasks-orphanblkn ) then
write(6,*) "thread:",i,"is for",taskpiece+1,"fine blocks."
endif
enddo
endif
taskpiece = myblkend - myblkstart + 1
myh = savh(2)
mingrdblk=min(ngrdblkx,ngrdblky,ngrdblkz)
if ( buffer/myh > mingrdblk ) then
write(6,*) "Big padding",int(buffer/myh), &
"is unrealistic (the least grdblk is", &
mingrdblk,"), please give up."
endif
if (mingrdblk == 0) then
write(*,*) "grdblkx or y, z contains zero."; stop
endif
! Possible problem: mjhsieh forgot why there is a "+ 2"
myldim=ceiling(2 + (buffer*2/myh/(mingrdblk-1)+3)**3) * natom
myldim=min(myldim,mynblock*natom)
! Multithread situation is not considered so far, thus no benifit
! from multithread to reducing array sizes "for now".
allocate(lfocuswpad(myldim), stat=ierr); if (ierr /= 0) call mexit(6,1)
allocate(lfocus0pad(2*natom+1), stat=ierr); if (ierr /= 0) call mexit(6,1)
allocate(lfocus4s3f(myldim), stat=ierr); if (ierr /= 0) call mexit(6,1)
lfocus4s3f = 0 !initialization
lfocuswpad = 0 !initialization
lfocus0pad = 0 !initialization
nfirst4s3f = 0 !initialization
nfirstwpad = 0 !initialization
nfirst0pad = 0 !initialization
! Following part initializes for level one
nfirst4s3f(1) = 1
nfirstwpad(1) = 1
nfirst0pad(1) = 1
! Grid Partition for Level 2
! lfocuswpad, lfocus0pad, nfirstwpad and nfirst0pad got updated
call pb_atmpart_mb(pbverbose, pbprint, natom, 1, mynblock, myh,&
blknx, blkny, blknz, blkxlo, blkylo, blkzlo, &
blkxup, blkyup, blkzup, blkgox, blkgoy, blkgoz, &
x, lfocuswpad, lfocus0pad, lfocus4s3f, &
nfirstwpad, nfirst0pad, nfirst4s3f, master)
! So the information needed for the solver are:
! myblkstart: the first block for focus finegrid in this thread
! myblkend: the last block for focus finegrid in this thread
! lfocuswpad: serial number list of the atoms covered by the
! focus fine grid with the padding zone
! lfocus0pad: serial number list of the atoms covered by the
! focus fine grid without the padding zone
! lfocus4s3f: atom list for doing surface for blocks
! nfirstwpad: the first position in lfocuswpad that belongs to
! current block (level 2 blocks start from 2)
! nfirst0pad: the first position in lfocus0pad that belongs to
! current block (level 2 blocks start from 2)
! nfirst4s3f: the first position in lfocus4s3f
tasknatom = nfirst0pad(mynblock+1)-nfirst0pad(1)
if ( tasknatom .ne. natom ) then
write(6, *) 'pb_force(): Atom partition error',tasknatom,'/=',natom
call mexit(6, 1)
endif
end if
call pbtimer_stop(PBTIME_PBLIST)
! for focussing run, liveflag, outflag, realflag are updated
! atom list is updated next
! surface area is then updated
if ( ligand ) then
call pb_atmlist(pbverbose,pbprint,maxnba,natom,ntypes,iac,ico,natex, &
nshrt,nex,iex,iar1pb,iprshrt,cutnb,cutsa,cutfd,cn1,cn2,cn1pb, &
cn2pb,cn3pb,cg,acrd)
call sa_driver(pbverbose,pbprint,ipb,inp,natom,natom,dosas,ndosas, &
npbstep,nsaslag,ligand,outflag,acrd(1,1),iar1pb(1,0),iprshrt, &
nex,iex)
! BEGIN OF MULTIPLE BLOCK LOOP: LOOPING OVER BLOCKS
else if ( multiblock ) then
! fineblockindex: storing the order of the multiblock for
! load balancing or just sequential order
allocate( fineblockindex(levelblock(2)), stat = ierr )
do i = 1, levelblock(2)
fineblockindex(i)=i
enddo
! This will shuffle the order, which is a fake load balancing.
call amrset(8249562)
if ( master ) then
allocate( tmpindex(levelblock(2)), stat = ierr )
do i = 1, levelblock(2)
call amrand(guess_float) ! from 0 to 1
guess_float = guess_float * (levelblock(2)+1-i)
guess_int = ceiling(guess_float)
ipermute = fineblockindex(guess_int)
fineblockindex(guess_int) = fineblockindex(levelblock(2)+1-i)
fineblockindex(levelblock(2)+1-i) = ipermute
enddo
tmpindex=fineblockindex
! Sort the list according to block gridsize (disabled)
! To enable it, you need to verify the index with the new scheme.
! do while (boolsorted == 0)
! boolsorted = 1
! do i = 2, levelblock(2)
! if (blknxnynz(tmpindex(i-1)) < blknxnynz(tmpindex(i))) then
! ipermute =tmpindex(i-1)
! tmpindex(i-1)=tmpindex(i )
! tmpindex(i )=ipermute
! boolsorted = 0
! endif
! enddo
! enddo
!distributing blocks among available nodes
k = 1
do i = 0, numtasks-1
do j = 1, levelblock(2)
if ( mod(j,numtasks) == i ) then
fineblockindex(k)=tmpindex(j)
k = k + 1
endif
enddo
enddo
deallocate( tmpindex, stat = ierr )
ihavedone = 0
endif
#ifdef MPI
#ifndef SANDER
! broadcast the ownership of blocks to each thread
call MPI_BCAST(fineblockindex(1),levelblock(2),MPI_INTEGER,0,CommSANDER,ierr)
REQUIRE(ierr==0)
!call MPI_BARRIER( CommSANDER, ierr );REQUIRE(ierr==0)
#endif
#endif /*MPI*/
!#ifdef MPI
! call mpi_bcast(fineblockindex,mynblock,MPI_INTEGER,0,commsander,ierr)
!#endif
! add FD reaction field energy/force
call pbtimer_start(PBTIME_PBFDFRC)
blk_eelrffd = ZERO
blk_eel = ZERO
blk_enb = ZERO
allocate(coarsephi(savxmymzm(1)), stat = ierr)
blkloop: do iblock=1, levelblock(2)
iblkdebug = iblock
indexmatched = .false.
matchingindex: do i = myblkstart, myblkend
if ( iblock == fineblockindex(i) ) then
indexmatched = .true.
cycle matchingindex
end if
end do matchingindex
if ( .not. indexmatched ) cycle blkloop
liveflag = 0 ! 1 if inside the block w/o pad
realflag = 0 ! 1 if inside the block with pad
outflag = 1 ! 1 if outside the geometry for surface
do i = nfirst0pad(iblock), nfirst0pad(iblock+1)-1
liveflag( lfocus0pad(i) ) = 1
end do
do i = nfirstwpad(iblock), nfirstwpad(iblock+1)-1
realflag( lfocuswpad(i) ) = 1
end do
do i = nfirst4s3f(iblock), nfirst4s3f(iblock+1)-1
outflag ( lfocus4s3f(i) ) = 0
end do
savxm(2)=blknx(iblock)
savym(2)=blkny(iblock)
savzm(2)=blknz(iblock)
savxmym(2)=blknxny(iblock)
savxmymzm(2)=blknxnynz(iblock)
savgox(2)=blkgox(iblock)
savgoy(2)=blkgoy(iblock)
savgoz(2)=blkgoz(iblock)
!write(600+mytaskid,*)maxnba,natom,ntypes,iac(1:natom),ico(1:ntypes*ntypes),natex(1:392);call mexit(0,0)
!write(600+mytaskid,*)nshrt(0:natom),nex(natom),iex(1:64,1:natom),iar1pb(1:6,0:natom);call mexit(0,0)
!write(600+mytaskid,*)iprshrt(maxnba),cutnb,cutsa,cutfd,cn1(1:1830),cn2(1:1830),cn1pb(1:maxnba);call mexit(0,0)
!write(600+mytaskid,*)cn2pb(1:maxnba),cn3pb(1:maxnba),cg,acrd(1:3,1:natom);call mexit(0,0)
call pb_atmlist(pbverbose,pbprint,maxnba,natom,ntypes,iac,ico,natex, &
nshrt,nex,iex,iar1pb,iprshrt,cutnb,cutsa,cutfd,cn1,cn2,cn1pb, &
cn2pb,cn3pb,cg,acrd)
!write(600+mytaskid,*)cn3pb(1:maxnba),cg,acrd(1:3,1:natom);call mexit(0,0)
!write(600+mytaskid,*)cn1(1:1830),cn2(1:1830),cn1pb(1:maxnba),cn2pb(1:maxnba);call mexit(0,0)
!write(600+mytaskid,*)iar1pb(1:6,0:natom),iprshrt(maxnba),cutnb,cutsa,cutfd;call mexit(0,0)
!write(600+mytaskid,*)ntypes,iac(1:natom),ico(1:ntypes*ntypes),natex(1:392),nshrt(0:natom),nex(natom),iex(1:64,1:natom);call mexit(0,0)
!write(600+mytaskid,*)ntypes,iac(1:natom),ico(1:ntypes*ntypes),natex(1:392),nshrt(0:natom),nex(natom),iex(1:64,1:natom);call mexit(0,0)
! In this implementation of multiblock focusing, each block is treated
! as exactly like a ligand box, so we hijack the ligand flag for now.
! Here is the interface before the hijack:
! call sa_driver(pbverbose,pbprint,ipb,inp,natom,natom,dosas,ndosas, &
! npbstep,nsaslag,ligand,outflag,acrd(1,1),iar1pb(1,0),iprshrt, &
! nex,iex)
call sa_driver(pbverbose,pbprint,ipb,inp,natom,natom,dosas,ndosas, &
npbstep,nsaslag,.true.,outflag,acrd(1,1),iar1pb(1,0),iprshrt, &
nex,iex)
!write(600+mytaskid,*)dosas,ndosas,npbstep,nsaslag,outflag(1:natom),acrd(1:3,1:natom);call mexit(0,0)
!write(600+mytaskid,*)iar1pb(1:6,0:natom),iprshrt(1:maxnba),nex(1:natom),iex(1:64,1:natom);call mexit(0,0)
! End of sa_driver hijack.
call pb_fdfrc(pbverbose,pbprint,pbgrid,ifcap,ipb,imin,natom,natom, &
npdec,idecomp,irespw,ipres,jgroup,ibgwat,ibgion,pbfrc, &
eelrffd,ionene,npbstep,npbgrid,nstlim)
blk_eelrffd = blk_eelrffd + eelrffd
ihavedone = ihavedone + 1
if ( srsas .and. ihavedone < taskpiece ) then
call sa_free_mb( dosas,ndosas )
end if
! cutnb > 0 is required in multiblock
!if ( cutnb == ZERO ) then
! call pb_directnocut(natom,proatm,inatm,ipres,ibgwat,ienwat,ibgion,ienion,ntypes,eneopt,idecomp,ifcap, &
! iac,ico,nex,iex,cn1,cn2,acg,acrd(1,1),pbfrc,eel,enb)
!else
if( ifcap == 2 .or. ifcap == 5) then
call pb_directwtcut(natom,inatm,ifcap,idecomp,iprshrt,iar1pb,cn1pb,cn2pb,cn3pb,acrd(1,1), &
pbfrc,eel,enb)
else
call pb_directwtcut(natom,natom,ifcap,idecomp,iprshrt,iar1pb,cn1pb,cn2pb,cn3pb,acrd(1,1), &
pbfrc,eel,enb)
end if
!endif
blk_eel = blk_eel + eel
blk_enb = blk_enb + enb
end do blkloop
deallocate (coarsephi, stat = ierr)
outflag = 0
realflag = 1
eelrffd = blk_eelrffd
eel = blk_eel
enb = blk_enb
! PHI MAP SHOULD BE EXPORTED IN FDFRC, NOT HERE.
! To do so xs is required for assembling the phi
call pbtimer_stop(PBTIME_PBFDFRC)
#ifdef MPI
#ifndef SANDER
allocate(recvbuf1(numtasks), stat = ierr); recvbuf1 = ZERO
allocate(recvbuf2(numtasks), stat = ierr); recvbuf2 = ZERO
allocate(recvbuf3(numtasks), stat = ierr); recvbuf3 = ZERO
call MPI_GATHER(eelrffd, 1, MPI_DOUBLE_PRECISION, recvbuf1, 1, &
MPI_DOUBLE_PRECISION, 0, CommSANDER, ierr)
call MPI_GATHER(eel , 1, MPI_DOUBLE_PRECISION, recvbuf2, 1, &
MPI_DOUBLE_PRECISION, 0, CommSANDER, ierr)
call MPI_GATHER(enb , 1, MPI_DOUBLE_PRECISION, recvbuf3, 1, &
MPI_DOUBLE_PRECISION, 0, CommSANDER, ierr)
if (master) then
eelrffd = SUM(recvbuf1)
eel = SUM(recvbuf2)
enb = SUM(recvbuf3)
endif
#endif
#endif /* MPI */
end if
! HERE GOES THE ENERGY SUMMATION (parallel)
! END OF MULTIPLE BLOCK LOOP
! add FD reaction field energy/force
call pbtimer_start(PBTIME_PBFDFRC)
if ( multiblock ) then
! For multiblock focusing, FD force is already done in the previous
! section. But that's not the case for ligand.
continue
else if ( epsout /= epsin .and. mpopt /= 2 ) then
! In the case of ifcap == 2,5, only map crg within cap to grid (atmlast == inatm),
! else map all crg (atmlast == natom)
if( ifcap == 2 .or. ifcap == 5 ) then
call pb_fdfrc(pbverbose,pbprint,pbgrid,ifcap,ipb,imin,natom,inatm,npdec,idecomp,irespw, &
ipres,jgroup,ibgwat,ibgion,pbfrc,eelrffd,ionene,npbstep,npbgrid,nstlim)
else
call pb_fdfrc(pbverbose,pbprint,pbgrid,ifcap,ipb,imin,natom,natom,npdec,idecomp,irespw, &
ipres,jgroup,ibgwat,ibgion,pbfrc,eelrffd,ionene,npbstep,npbgrid,nstlim)
end if
end if
call pbtimer_stop(PBTIME_PBFDFRC)
! clean up for sas calculations
call pbtimer_start(PBTIME_PBSETUP)
if ( srsas .and. (ifcap == 0 .or. ifcap == 5) ) then
call sa_free( dosas,ndosas )
end if
call pbtimer_stop(PBTIME_PBSETUP)
if ( saopt < 0 ) return
! add MP reaction field energy/forces when ifcap /= 0
call pbtimer_start(PBTIME_PBMP)
if ( mpopt /= 0 .and. epsout /= epsin ) then
if ( mpopt == 1 ) then ! multipole expansion for boundary atoms
atmfirst = inatm + 1
atmlast = natom
else if ( mpopt == 2 ) then ! multipole expansion for all atoms
atmfirst = 1
atmlast = natom
end if
call pb_mpfrc(natom,atmfirst,atmlast,lmax,pbcutcap,pbxcap,pbycap,pbzcap,&
epsin,epsout,acrg,acrd(1,1),pbfrc,eelrfmp)
end if
call pbtimer_stop(PBTIME_PBMP)
! add direct coulombic and nonbonded forces
call pbtimer_start(PBTIME_PBDIRECT)
if ( multiblock ) then
! For multiblock focusing, pb_direct SHOULD BE DONE inside the loop
continue
else if ( cutnb == ZERO ) then
call pb_directnocut(natom,proatm,inatm,ipres,ibgwat,ienwat,ibgion,ienion,ntypes,eneopt,idecomp,ifcap, &
iac,ico,nex,iex,cn1,cn2,acg,acrd(1,1),pbfrc,eel,enb)
else
if( ifcap == 2 .or. ifcap == 5) then
call pb_directwtcut(natom,inatm,ifcap,idecomp,iprshrt,iar1pb,cn1pb,cn2pb,cn3pb,acrd(1,1), &
pbfrc,eel,enb)
else
call pb_directwtcut(natom,natom,ifcap,idecomp,iprshrt,iar1pb,cn1pb,cn2pb,cn3pb,acrd(1,1), &
pbfrc,eel,enb)
end if
end if
call pbtimer_stop(PBTIME_PBDIRECT)
! returning:
! adding the nonbonded forces to the MD forces
if ( eneopt == 1 .and. bcopt < 6 ) then
eel = eel + eelrffd + eelrfmp
eelrf = ZERO
if ( pbverbose .and. master ) &
write(6,'(a,F21.10)') '| ERF = ',eelrffd+eelrfmp
else
eelrf = eelrffd + eelrfmp
end if
if( ifcap == 2 .or. ifcap == 5 ) then
atmlast = inatm
else
atmlast = natom
endif
do iatm = 1, natom
f(1,iatm) = f(1,iatm) + pbfrc(1,mapout(iatm))
f(2,iatm) = f(2,iatm) + pbfrc(2,mapout(iatm))
f(3,iatm) = f(3,iatm) + pbfrc(3,mapout(iatm))
end do
! open (unit = 120, file = 'total.dat')
! write(120,*) ' :::: Atomic forces ::::'
! do iatm = 1, natom
! write(120,'(3e20.6)') f(1,iatm),f(2,iatm),f(3,iatm)
! end do
! open (unit = 121, file = 'total2.dat')
! write(121,*) ' :::: Atomic forces ::::'
! do iatm = 1, natom
! write(121,'(3e20.6)') pbfrc(1,iatm),pbfrc(2,iatm),pbfrc(3,iatm)
! end do
contains
!+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
!+ convert passed coordinates and charges to the internal format
subroutine pb_atmconv( mpopt,ifcap,natom,ibgwat,ienwat,ibgion,ienion,atmind,ipres,x,cg,acg )
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!
! Authors:
! Lijiang Yang, Luo Research Group, UC-Irvine
!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
! Passed variables
integer mpopt, ifcap, natom, ibgwat, ienwat, ibgion, ienion
integer atmind(natom), ipres(*)
_REAL_ x(3,natom), cg(natom), acg(natom)
! Local variables
integer i, j, ifirst, ilast, iatm, ires, num
if ( mpopt == 1 .or. ifcap == 2 .or. ifcap == 5 ) then
! copy reordered coord/charge to private arrays for pb/mp or ifcap == 2,5
! protein atoms go into internal portion (so do IONS!)
ifirst = 1; ilast = ipres(ibgwat)-1
do iatm = ifirst, ilast
acrd(1,iatm) = x(1,iatm); acrd(2,iatm) = x(2,iatm); acrd(3,iatm) = x(3,iatm)
acrg(iatm) = cg(iatm)/18.2223d0; acg(iatm) = cg(iatm); atmind(iatm) = iatm
mapout(iatm) = iatm
end do
! water atoms go into internal/external portion
ifirst = ipres(ibgwat); ilast = natom
i = ifirst; j = inatm + 1
do iatm = ifirst, ilast
if ( outflag(iatm) == 0 ) then
acrd(1,i ) = x(1,iatm); acrd(2,i ) = x(2,iatm); acrd(3,i ) = x(3,iatm)
acrg(i ) = cg(iatm)/18.2223d0; acg(i ) = cg(iatm); atmind(i ) = iatm
mapout(iatm) = i
i = i + 1
else
acrd(1,j ) = x(1,iatm); acrd(2,j ) = x(2,iatm); acrd(3,j ) = x(3,iatm);
acrg(j ) = cg(iatm)/18.2223d0; acg(j ) = cg(iatm); atmind(j ) = iatm
mapout(iatm) = j
j = j + 1
end if
end do
! store original outflag array and prepare an updated one for water atoms
outflagorig = outflag
do iatm = ifirst, ilast
if( iatm <= inatm ) then
outflag(iatm) = 0
else
outflag(iatm) = 1
end if
end do
else
do iatm = 1, natom
acrd(1,iatm) = x(1,iatm); acrd(2,iatm) = x(2,iatm); acrd(3,iatm) = x(3,iatm)
acrg(iatm) = cg(iatm)/18.2223d0; acg(iatm) = cg(iatm)
mapout(iatm) = iatm
end do
end if
end subroutine pb_atmconv
end subroutine pb_force
!+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
!+ driver for FDPB forces and energy
subroutine pb_fdfrc( pbverbose,pbprint,pbgrid,ifcap,ipb,imin,natom,atmlast,npdec,idecomp,irespw, &
ipres,jgroup,ibgwat,ibgion,pbfrc,eelrf,ionene,npbstep,npbgrid,nstlim )
use solvent_accessibility, only : dprob,iprob,radi,radip3,nzratm, &
narcdot,maxarc,marc,m2narc,fstarc,arcatm,arccrd,savarc,dotarc
!#ifndef SANDER
use pbtimer_module
!#endif
# include "flocntrl.h"
#include "parallel.h"
! passed variables
logical pbverbose, pbprint, pbgrid
integer ifcap, ipb, imin, natom, atmlast, npdec, idecomp, ibgwat, ibgion
integer npbstep, npbgrid, nstlim
integer irespw(*), ipres(*), jgroup(*)
_REAL_ ionene, eelrf, pbfrc(3,natom)!, fnet(3)
! local variables
integer atmfirst
integer iatm, lastatm, mpdec, i
_REAL_ eelself, eelcoul, rh, fcrd(3,atmlast)
_REAL_ aa, bb, cc, aa1, bb1, cc1
_REAL_ bb1cc1, bb_cc1, bb1cc, bb_cc
_REAL_ acrgtmp, factor
if ( do_pbfd == 0 ) return
mpdec = 1
if ( idecomp > 2 ) mpdec = npdec
!-- PB pairwise decomp <<1,mpdec>>
atmfirst = 1
! atmfirst is supposedly to be passed
do m = 1, mpdec
! do fdpb calculations upto nfocus